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Remove most stability/suitability/experimental warnings #2120

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e0d2355
Remove most stability/suitability/experimental warnings
mattwthompson Nov 6, 2025
09af85a
Update release history
mattwthompson Nov 6, 2025
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4 changes: 4 additions & 0 deletions docs/releasehistory.md
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Expand Up @@ -9,6 +9,10 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w

## Current development

### Miscellaneous

- [PR #2XXX](https://github.com/openforcefield/openff-toolkit/pull/2XXX): Removes many duplicate warnings about API stability. (Versions starting with 0.x have no stability guarantees, though efforts are made to communicate major API breaks and behavior changes beforehand.)

### API-breaking changes

### Behavior changes
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6 changes: 1 addition & 5 deletions docs/users/molecule_cookbook.ipynb
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Expand Up @@ -1227,11 +1227,7 @@
"\n",
"Most `Molecule` creation methods don't specify the ordering of atoms in the new `Molecule`. The [`Molecule.remap()`](openff.toolkit.topology.Molecule.remap) method allows a new ordering to be applied to an existing `Molecule`.\n",
"\n",
"See also [](#mapped-smiles).\n",
"\n",
":::{warning}\n",
"The `Molecule.remap()` method is experimental and subject to change. \n",
":::"
"See also [](#mapped-smiles)."
]
},
{
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6 changes: 1 addition & 5 deletions examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb
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Expand Up @@ -6,11 +6,7 @@
"source": [
"# Inspect parameters assigned to specific molecules\n",
"\n",
"The Open Force Field Toolkit applies parameters based on the [SMARTS/SMIRKS language](http://www.daylight.com/dayhtml_tutorials/languages/smarts/). These examples are intended to expose how `ForceField` assigns SMIRKS-based parameters to test molecules.\n",
"\n",
"<div class=\"alert alert-block alert-warning\">\n",
" <b>Note:</b> This API is not final, and we will be implementing a better way to visualize assigned parameters in the future.\n",
"</div>"
"The Open Force Field Toolkit applies parameters based on the [SMARTS/SMIRKS language](http://www.daylight.com/dayhtml_tutorials/languages/smarts/). These examples are intended to expose how `ForceField` assigns SMIRKS-based parameters to test molecules."
]
},
{
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25 changes: 0 additions & 25 deletions openff/toolkit/topology/molecule.py
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Expand Up @@ -125,7 +125,6 @@ class Particle(Serializable):

A particle object could be an ``Atom`` or similar.

.. warning :: This API is experimental and subject to change.
"""

_molecule: "FrozenMolecule"
Expand Down Expand Up @@ -212,7 +211,6 @@ class Atom(Particle):
quantities (such as ``id`` or ``serial`` index in a PDB file),
or string labels (such as Lennard-Jones types)?

.. warning :: This API is experimental and subject to change.
"""

def __init__(
Expand Down Expand Up @@ -641,8 +639,6 @@ class Bond(Serializable):
"""
Chemical bond representation.

.. warning :: This API is experimental and subject to change.

.. todo :: Allow bonds to have associated properties.

Attributes
Expand All @@ -658,7 +654,6 @@ class Bond(Serializable):
stereochemstry
A string representing this stereochemistry of this bond.

.. warning :: This API is experimental and subject to change.
"""

def __init__(
Expand Down Expand Up @@ -889,8 +884,6 @@ class FrozenMolecule(Serializable):

>>> molecule = FrozenMolecule.from_smiles('Cc1ccccc1')

.. warning :: This API is experimental and subject to change.


"""

Expand Down Expand Up @@ -1995,8 +1988,6 @@ def are_isomorphic(
By default, all attributes are checked, but stereochemistry around
pyrimidal nitrogen is ignored.

.. warning :: This API is experimental and subject to change.

Parameters
----------
mol1
Expand Down Expand Up @@ -2191,8 +2182,6 @@ def is_isomorphic_with(
Check if the molecule is isomorphic with the other molecule which can be an openff.toolkit.topology.Molecule
or nx.Graph(). Full matching is done using the options described bellow.

.. warning :: This API is experimental and subject to change.

Parameters
----------
other
Expand Down Expand Up @@ -2727,8 +2716,6 @@ def assign_fractional_bond_orders(
Bond orders are stored on each bond, in the
``bond.fractional_bond_order`` attribute.

.. warning :: This API is experimental and subject to change.

Parameters
----------
toolkit_registry
Expand Down Expand Up @@ -4409,8 +4396,6 @@ def to_qcschema(self, multiplicity=1, conformer=0, extras=None):
* ``extras["canonical_isomeric_explicit_hydrogen_mapped_smiles"]``
* ``identifiers["canonical_isomeric_explicit_hydrogen_mapped_smiles"]``

.. warning :: This API is experimental and subject to change.

Parameters
----------
multiplicity
Expand Down Expand Up @@ -4503,8 +4488,6 @@ def from_mapped_smiles(
once; any duplicate, missing, or out-of-range mappings will cause the
method to fail.

.. warning :: This API is experimental and subject to change.

Parameters
----------
mapped_smiles: str
Expand Down Expand Up @@ -4750,8 +4733,6 @@ def from_pdb_and_smiles(

Requires RDKit to be installed.

.. warning :: This API is experimental and subject to change.

The molecule is created and sanitised based on the SMILES string, we then find a mapping
between this molecule and one from the PDB based only on atomic number and connections.
The SMILES molecule is then reindexed to match the PDB, the conformer is attached, and the
Expand Down Expand Up @@ -4799,8 +4780,6 @@ def canonical_order_atoms(self, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY):
order may change from toolkit version to toolkit version or between
toolkits.

.. warning :: This API is experimental and subject to change.

Parameters
----------
toolkit_registry
Expand Down Expand Up @@ -4851,8 +4830,6 @@ def remap(
the new ordering. Other values of the properties dictionary are
transferred unchanged.

.. warning :: This API is experimental and subject to change.

Parameters
----------
mapping_dict
Expand Down Expand Up @@ -5195,8 +5172,6 @@ class Molecule(FrozenMolecule):

>>> molecule = Molecule.from_smiles('Cc1ccccc1')

.. warning :: This API is experimental and subject to change.

"""

def __init__(self, *args, **kwargs):
Expand Down
2 changes: 0 additions & 2 deletions openff/toolkit/topology/topology.py
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Expand Up @@ -391,8 +391,6 @@ class Topology(Serializable):
A Topology is a chemical representation of a system containing one or more molecules appearing in a specified
order.

.. warning :: This API is experimental and subject to change.

Examples
--------

Expand Down
12 changes: 0 additions & 12 deletions openff/toolkit/typing/engines/smirnoff/forcefield.py
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Expand Up @@ -510,8 +510,6 @@ def _register_parameter_handler_classes(
"""
Register multiple ParameterHandler classes, ensuring they specify unique tags to process

.. warning :: This API is experimental and subject to change.

Parameters
----------
parameter_handler_classes
Expand All @@ -535,8 +533,6 @@ def _register_parameter_io_handler_classes(
"""
Register multiple ParameterIOHandler classes, ensuring they specify unique suffixes

.. warning :: This API is experimental and subject to change.

Parameters
----------
parameter_io_handler_classes
Expand Down Expand Up @@ -566,8 +562,6 @@ def register_parameter_handler(self, parameter_handler: ParameterHandler):
Register a new ParameterHandler for a specific tag, making it
available for lookup in the ForceField.

.. warning :: This API is experimental and subject to change.

Parameters
----------
parameter_handler
Expand All @@ -592,8 +586,6 @@ def register_parameter_io_handler(self, parameter_io_handler: ParameterIOHandler
"""
Register a new ParameterIOHandler, making it available for lookup in the ForceField.

.. warning :: This API is experimental and subject to change.

Parameters
----------
parameter_io_handler
Expand All @@ -614,8 +606,6 @@ def registered_parameter_handlers(self) -> list[str]:
"""
Return the list of registered parameter handlers by name

.. warning :: This API is experimental and subject to change.

Returns
-------
registered_parameter_handlers
Expand Down Expand Up @@ -1193,8 +1183,6 @@ def create_interchange(
"""
Create an Interchange object from a ForceField, Topology, and (optionally) box vectors.

WARNING: This API and functionality are experimental and not suitable for production.

Parameters
----------
topology
Expand Down
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